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### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD check --install=check:GenomeInfoDb.install-out.txt --library=/Library/Frameworks/R.framework/Resources/library --no-vignettes --timings GenomeInfoDb_1.36.4.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenomeInfoDb.Rcheck’
* using R version 4.3.1 (2023-06-16)
* using platform: aarch64-apple-darwin20 (64-bit)
* R was compiled by
    Apple clang version 14.0.0 (clang-1400.0.29.202)
    GNU Fortran (GCC) 12.2.0
* running under: macOS Monterey 12.6.7
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘GenomeInfoDb/DESCRIPTION’ ... OK
* this is package ‘GenomeInfoDb’ version ‘1.36.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘GenomeInfoDb’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Problems with news in ‘NEWS’:
  Cannot process chunk/lines:
    NEW FEATURES
  Cannot process chunk/lines:
    SIGNIFICANT USER-VISIBLE CHANGES
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking startup messages can be suppressed ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: ‘utils:::.roman2numeric’
  See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... OK
* checking Rd files ... WARNING
checkRd: (5) GenomeDescription-class.Rd:53-58: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:59-63: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:64-70: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:71-75: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:76-79: \item in \describe must have non-empty label
checkRd: (5) GenomeDescription-class.Rd:80-88: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:83-93: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:101-104: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:105-115: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:116-119: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:120-123: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:124-149: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:150-153: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:154-157: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:158-162: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:170-178: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:186-189: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:226-249: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:250-256: \item in \describe must have non-empty label
checkRd: (5) Seqinfo-class.Rd:257-262: \item in \describe must have non-empty label
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU (user + system) or elapsed time > 5s
                          user system elapsed
loadTaxonomyDb          10.707  0.251  16.746
GenomeDescription-class  8.133  0.356  12.095
seqlevels-wrappers       5.333  0.276   8.625
seqinfo                  5.045  0.348   8.161
getChromInfoFromUCSC     3.187  1.558   8.404
seqlevelsStyle           4.119  0.380  15.846
getChromInfoFromEnsembl  0.615  0.156  33.630
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘run_unitTests.R’
 OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.17-bioc-mac-arm64/meat/GenomeInfoDb.Rcheck/00check.log’
for details.

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Resources/bin/R CMD INSTALL GenomeInfoDb
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/4.3-arm64/Resources/library’
* installing *source* package ‘GenomeInfoDb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDb)

R version 4.3.1 (2023-06-16) -- "Beagle Scouts"
Copyright (C) 2023 The R Foundation for Statistical Computing
Platform: aarch64-apple-darwin20 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> require("GenomeInfoDb") || stop("unable to load GenomeInfoDb package")
Loading required package: GenomeInfoDb
Loading required package: BiocGenerics

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, aperm, append,
    as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
    pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
    tapply, union, unique, unsplit, which.max, which.min

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following object is masked from 'package:utils':

    findMatches

The following objects are masked from 'package:base':

    I, expand.grid, unname

Loading required package: IRanges
[1] TRUE
> GenomeInfoDb:::.test()


RUNIT TEST PROTOCOL -- Tue Oct 17 21:44:47 2023 
*********************************************** 
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 

 
1 Test Suite : 
GenomeInfoDb RUnit Tests - 21 test functions, 0 errors, 0 failures
Number of test functions: 21 
Number of errors: 0 
Number of failures: 0 
There were 50 or more warnings (use warnings() to see the first 50)
> 
> proc.time()
   user  system elapsed 
456.835  26.081 789.139